EP2844743B1 - Enhanced affinity t cell receptors and methods for making the same - Google Patents

Enhanced affinity t cell receptors and methods for making the same Download PDF

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EP2844743B1
EP2844743B1 EP13784884.2A EP13784884A EP2844743B1 EP 2844743 B1 EP2844743 B1 EP 2844743B1 EP 13784884 A EP13784884 A EP 13784884A EP 2844743 B1 EP2844743 B1 EP 2844743B1
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cells
tcr
peptide
cell
antigen
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EP2844743A1 (en
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Thomas M. Schmitt
Philip D. Greenberg
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Fred Hutchinson Cancer Center
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    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
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    • C12N2502/13—Coculture with; Conditioned medium produced by connective tissue cells; generic mesenchyme cells, e.g. so-called "embryonic fibroblasts"
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    • G01N2333/70503—Immunoglobulin superfamily, e.g. VCAMs, PECAM, LFA-3
    • G01N2333/7051—T-cell receptor (TcR)-CD3 complex

Definitions

  • TCR gene therapy is an emerging treatment approach that can overcome many of the obstacles associated with conventional T cell adoptive immunotherapy, such as the extensive time and labor required to isolate, characterize, and expand tumor antigen-specific T cell clones ( Schmitt, Ragnarsson, & Greenberg, 2009, Hum. Gene Ther. 20:1240-1248 ). Further benefits of gene therapy include the ability to utilize defined populations of T cells capable of long-term persistence in vivo ( Berger et al., 2008, J. Clin. Invest. 118:294-305 ; Hinrichs et al., 2009, Proc. Natl. Acad. Sci. USA 106:17469-17474 ).
  • T cells can be transduced with genes encoding well-characterized TCRs that have a high affinity for tumor antigens, thereby increasing the likelihood of mediating an antitumor effect.
  • a recent report of therapy targeting advanced B cell leukemia with genetically modified T cells expressing a high affinity chimeric receptor targeting a self/tumor-antigen has highlighted the potential of using engineered high avidity T cells for the treatment of leukemia ( Kalos et al., 2011, Sci. Transl. Med. 3:95ra73 ).
  • high affinity T cells specific for these antigens are generally subject to negative selection in the thymus. Therefore, one significant limitation of T cell based immunotherapies in general is the limited availability of T cells expressing an endogenous TCR with sufficiently high affinity for non-mutated tumor antigens.
  • CDR1 and CDR2 regions predominantly make contact with the MHC molecule, while the hypervariable CDR3 region primarily contacts the peptide ( Wucherpfennig et al., 2010, Cold Spring Harbor Perspectives in Biology 2:a005140-a005140 ).
  • Site-directed mutagenesis strategies generally target selected portions of all three of these regions, but still are not always successful in generating a higher affinity variant, and the improvements are limited to changes only in the specifically targeted regions.
  • mutations introduced into the MHC contact residues have the risk of potentially increasing the affinity of the TCR for MHC while decreasing the overall specificity of the receptor for its cognate peptide.
  • most mutations introduced to enhance the affinity of a TCR would be restricted to the CDR3 region for this reason.
  • current methodologies are limited in the capacity to generate CDR3 diversity, because site-directed mutagenesis is constrained by the original length of the CDR3 region.
  • enhanced affinity T cell receptor refers to a selected or engineered TCR with stronger binding to a target antigen than the wild type (or parent) TCR.
  • thymocyte progenitor cell or "thymocyte” is a hematopoietic progenitor cell present in the thymus.
  • cells of the T cell lineage may be progenitor or precursor cells committed to the T cell lineage; CD25 + immature and inactivated T cells; cells that have undergone CD4 or CD8 linage commitment; thymocyte progenitor cells that are CD4 + CD8 + double positive; single positive CD4 + or CD8 + ; TCR ⁇ or TCR ⁇ ; or mature and functional or activated T cells.
  • stromal cells are connective tissue cells of any organ.
  • the stromal cells are bone marrow stromal cells.
  • Examples of stromal cell lines that can be engineered to express DLL1 or DLL4 include the mouse stromal cell line MS5 ( Itoh, et al., Exp. Hematol. 1989, 17:145-153 ) and S17, and the human stromal cell lines HGS2.11, HGS2.52, HGS.18, HGS3.30, HGS3.65, HGS.3.66, HGS3.103, and HGS3.114 (available from Human Genome Sciences Inc., MD, see US Published Application 20020001826 ).
  • OP9 cells Kodama et al., 1994, Exp.
  • Non-endogenous refers to a molecule (e.g ., nucleic acid sequence) that is not present in the host cell(s)/sample into which a molecule is introduced, for example, recombinantly introduced.
  • a non-endogenous molecule may be from the same species or a different species.
  • NM_007865.3 SEQ ID NO:5
  • NP_031891.2 SEQ ID NO:6
  • Exemplary Delta-like-4 sequences include Genbank Accession No. NM_019074.3 (SEQ ID NO:7) and NP_061947.1 (SEQ ID NO:8) ( Homo sapiens transcript and protein sequences, respectively) and Genbank Accession No. NM_019454.3 (SEQ ID NO:9) and NP_062327.2 (SEQ ID NO:10) ( Mus musculus transcript and protein sequences, respectively).
  • Notch ligands are commercially available or can be produced by standard recombinant DNA techniques and purified to various degrees.
  • Exemplary mesothelin sequences include Genbank Accession Nos: NM_001177355.1 (SEQ ID NO:23), NP_001170826.1 (SEQ ID NO:24) (human transcript and pre-protein sequences, respectively); NM_005823.5 (SEQ ID NO:25), NP_005814.2 (SEQ ID NO:26)(human transcript and pre-protein sequences, respectively); NM_013404.4 (SEQ ID NO:27), NP_037536.2 (SEQ ID NO:28) (human transcript and pre-protein sequences, respectively); NM_018857.1 (SEQ ID NO:29), NP_061345.1 (SEQ ID NO:30) (mouse transcript and precursor protein sequences, respectively).
  • This receptor is called the Pre-TCR, and it signals in a ligand-independent fashion to promote proliferation, differentiation of ⁇ lineage cells to the CD4/CD8 double positive (DP) stage, and rearrangement at the Tcra gene locus ( Boehmer et al., 1999, Curr. Opin. Immunol. 11:135-142 ).
  • the hematopoietic progenitor cells have been modified to comprise a non-endogenous nucleic acid sequence encoding a TCR ⁇ chain from a parent TCR specific for the peptide antigen.
  • the TCR ⁇ chain is also isolated from the parent TCR.
  • Cloning of TCR ⁇ and ⁇ chains may be performed using standard molecular biology techniques that are known in the art. Methods for cloning TCR chains are known in the art ( see, e.g., Walchli et al., 2011, PLoS ONE 6:e27930 ; Birkholz et al., 2009, J. Immunol. Methods 346:45-54 ; Kurokawa et al, 2001, Clin. Exp. Immunol. 123:340-345 ).
  • stromal cells comprise non-endogenous nucleic acid sequences encoding DL1, such as human DL1.
  • Exemplary Delta-like-1 sequences include Genbank Accession No. NM_005618.3 (SEQ ID NO:3) and NP_005609.3 (SEQ ID NO:4) ( Homo sapiens transcript and protein sequences, respectively) and Genbank Accession No. NM_007865.3 (SEQ ID NO:5) and NP_031891.2 (SEQ ID NO:6) ( Mus musculus transcript and protein sequences, respectively).
  • stromal cells comprise non-endogenous nucleic acid sequences encoding DL4, such as human DL4.
  • Exemplary Delta-like-4 sequences include Genbank Accession No.
  • stromal cells are OP9 cells or a derivative thereof expressing DL1, such as human DL1.
  • OP9 cells expressing DL1 and DL4 have been previously described ( Schmitt et al., 2002, Immunity 17:749-756 ; U.S. Patent No. 7,575,925 ).
  • stromal cells also comprise a nucleic acid sequence encoding an MHC molecule.
  • stromal cells comprise a nucleic acid sequence encoding an MHC Class I molecule, and may optionally also comprise a nucleic acid sequence encoding a ⁇ 2 microglobulin.
  • the MHC Class I and ⁇ 2 microglobulin molecules may be derived from human, mouse, rat, or other mammalian species MHC Class I molecules, whose genes and protein sequences are known in the art.
  • the stromal cells comprise a nucleic acid sequence encoding an MHC Class II molecule.
  • the MHC Class II molecule may be derived from human, mouse, rat, or other mammalian species MHC molecules, whose genes and protein sequences are known in the art.
  • a given T cell will recognize a peptide antigen only when it is bound to a host cell's MHC molecule (MHC-restricted antigen recognition).
  • MHC-restricted antigen recognition A parent TCR with specificity for a known peptide antigen is selected for enhancement of the TCR affinity using the disclosed methods. Therefore, an MHC molecule that binds the particular peptide antigen is also selected and expressed in the stromal cells to allow MHC-restricted antigen recognition in the disclosed in vitro system.
  • Methods for identifying an MHC molecule that binds a peptide antigen are known in the art (see, e.g. , Akatsuka et al., 2002, Tissue Antigens 59:502-511 ).
  • H-2D b restricted mesothelin epitopes disclosed in Hung et al. include: ISKANVDVL (SEQ ID NO:42), GQKMNAQAI (SEQ ID NO:43), SAFQNVSGL (SEQ ID NO:44), and LLGPNIVDL (SEQ ID NO:45).
  • Potential H-2Kb restricted mesothelin epitopes disclosed in Hung et al. include: EIPFTYEQL (SEQ ID NO:46) and GIPNGYLVL (SEQ ID NO:47).
  • a “vector” is a nucleic acid molecule that is capable of transporting another nucleic acid.
  • Vectors may be, for example, plasmids, cosmids, viruses, or phage.
  • An "expression vector” is a vector that is capable of directing the expression of a protein encoded by one or more genes carried by the vector when it is present in the appropriate environment.
  • a vector that encodes a core virus is also known as a "viral vector.”
  • viral vectors There are a large number of available viral vectors that are suitable for use with the invention, including those identified for human gene therapy applications, such as those described by Pfeifer and Verma ( Pfeifer, A. and I. M. Verma. 2001. Ann. Rev. Genomics Hum. Genet. 2:177-211 ).
  • Suitable viral vectors include vectors based on RNA viruses, such as retrovirus-derived vectors, e.g. , Moloney murine leukemia virus (MLV)-derived vectors, and include more complex retrovirus-derived vectors, e.g ., lentivirus-derived vectors. HIV-1-derived vectors belong to this category.
  • lentivirus vectors derived from HIV-2, FIV, equine infectious anemia virus, SIV, and maedi/visna virus include lentivirus vectors derived from HIV-2, FIV, equine infectious anemia virus, SIV, and maedi/visna virus.
  • Methods of using retroviral and lentiviral viral vectors and packaging cells for transducing mammalian target cells with viral particles containing TCRs transgenes are well known in the art and have been previous described, for example, in U.S. Patent 8,119,772 ; Walchli et al., 2011, PLoS One 6:327930 ; Zhao et al., J. Immunol., 2005, 174:4415-4423 ; Engels et al., 2003, Hum. Gene Ther.
  • Retroviral and lentiviral vector constructs and expression systems are also commercially available.
  • a viral vector is used to introduce the non-endogenous nucleic acid sequence encoding TCR ⁇ chain specific for the peptide antigen into the hematopoietic progenitor cells.
  • a viral vector is used to introduce non-endogenous nucleic acid sequence encoding DL1 or DL4 and a nucleic acid sequence encoding an MHC molecule into stromal cells.
  • the viral vector may be a retroviral vector or a lentiviral vector.
  • the viral vector may also include a nucleic acid sequence encoding a marker for transduction.
  • Transduction markers for viral vectors are known in the art and include selection markers, which may confer drug resistance, or detectable markers, such as fluorescent markers or cell surface proteins that can be detected by methods such as flow cytometry.
  • the viral vector further comprises a gene marker for transduction comprising green fluorescent protein or the extracellular domain of human CD2.
  • the viral vector genome comprises more than one nucleic acid sequence to be expressed in the host cell as separate transcripts
  • the viral vector may also comprise additional sequence between the two (or more) transcripts allowing bicistronic or multicistronic expression. Examples of such sequences used in viral vectors include internal ribosome entry sites (IRES), furin cleavage sites, viral 2A peptide.
  • vectors also can be used for polynucleotide delivery including DNA viral vectors, including, for example adenovirus-based vectors and adeno-associated virus (AAV)-based vectors; vectors derived from herpes simplex viruses (HSVs), including amplicon vectors, replication-defective HSV and attenuated HSV ( Krisky et al., 1998, Gene Ther. 5: 1517-30 ).
  • DNA viral vectors including, for example adenovirus-based vectors and adeno-associated virus (AAV)-based vectors
  • HSVs herpes simplex viruses
  • amplicon vectors including amplicon vectors, replication-defective HSV and attenuated HSV ( Krisky et al., 1998, Gene Ther. 5: 1517-30 ).
  • vectors that have recently been developed for gene therapy uses can also be used with the methods of this disclosure.
  • Such vectors include those derived from baculoviruses and alpha-viruses. ( Jolly D J. 1999. Emerging viral vectors. pp 209-40 in Friedmann T. ed. 1999 . The development of human gene therapy. New York: Cold Spring Harbor Lab ).
  • the hematopoietic progenitor cells are cultured with stromal cells comprising a nucleic acid sequence encoding a non-endogenous DL1 or DL4 and a nucleic acid sequence encoding a MHC molecule under conditions and for a time sufficient to induce differentiation of hematopoietic progenitor cells into DN TCR ⁇ + thymocytes.
  • the hematopoietic progenitor cells are cultured in a 6 cm or 10 cm tissue culture-treated dish.
  • the concentration of hematopoietic progenitor cells in the culture can be between 1-10 9 , or 1x10 2 to 1x10 6 , or 1x10 3 to 1x 10 4 .
  • hematopoietic progenitor cells (about 1-5 x 10 4 cells) are cultured on a monolayer of OP9 cells expressing DL1.
  • cytokines that promote commitment and differentiation of hematopoietic progenitor cells may also be added to the culture.
  • the cytokines may be derived from human or other species.
  • the concentration of a cytokine in culture can range from about 1 ng/ml to about 50 ng/ml.
  • Representative examples of cytokines that may be used include: all members of the FGF family, including FGF-4 and FGF-2; Flt-3-ligand, stem cell factor (SCF), thrombopoietin (TPO), and IL-7.
  • Cytokines may be used in combination with a glycosaminoglycan, such as heparin sulfate. Cytokines are commercially available or can be produced by recombinant DNA techniques and purified to various degrees. Some cytokines may be purified from culture media of cell lines by standard biochemical techniques.
  • the hematopoietic progenitor cells may be cultured in culture medium comprising conditioned medium, non-conditioned medium, or embryonic stem cell medium.
  • suitable conditioned medium include IMDM, DMEM, or ⁇ MEM, conditioned with embryonic fibroblast cells ( e.g ., human embryonic fibroblast cells), or equivalent medium.
  • suitable non-conditioned medium include Iscove's Modified Delbucco's Medium (IDMD), DMEM, or ⁇ MEM, or equivalent medium.
  • the culture medium may comprise serum (e.g ., bovine serum, fetal bovine serum, calf bovine serum, horse serum, human serum, or an artificial serum substitute) or it may be serum free.
  • Culture conditions entail culturing the hematopoietic progenitor cells for a sufficient time to induce differentiation of hematopoietic progenitor cells into DN TCR ⁇ + thymocytes.
  • the cells are maintained in culture generally for about 4-5 days, preferably about 5 to 20 days. It will be appreciate that the cells may be maintained for the appropriate amount of time required to achieve a desired result, i.e., desired cellular composition.
  • the cells may be maintained in culture for about 5 to 20 days.
  • Cells may be maintained in culture for 20 to 30 days to generate a cellular composition comprising primarily mature T cells.
  • Non-adherent cells may also be collected from culture at various time points, such as from about several days to about 25 days. Culture methods for hematopoietic stem cells on stromal cells lines have been previously described ( U.S. Patent #7,575,925 ; Schmitt et al., 2004, Nat. Immunol. 5:410-417 ; Schmitt et al., 2002, Immunity 17:749-756 ).
  • Differentiation of hematopoietic progenitor cells into DN TCR ⁇ + thymocytes may be detected and these cells isolated using standard flow cytometry methods.
  • One or more cell sorts may be employed to isolate the DN TCR ⁇ + thymocytes.
  • a first cell sort may identify hematopoietic progenitor cells expressing the transduction marker (i.e., marker for TCR ⁇ expression).
  • a transduction marker is the extracellular domain of human CD2.
  • transduction marker positive cells may be subjected to a second cell sort to screen for cells that are CD4 - and CD8 - .
  • a third cell sort on the DN cells may screen for cells expressing TCR ⁇ .
  • the nucleic acid sequences encoding the various TCR ⁇ chains from the DN TCR ⁇ + thymocytes are isolated and introduced into T cells comprising the nucleic acid sequence encoding the TCR ⁇ chain from the parent TCR.
  • methods of cloning TCR ⁇ chains from cells are well known in the art and have been previously described.
  • the nucleic acid sequences may be subjected to a further selection process whereby the TCR ⁇ chains with the same V ⁇ gene used by the parent TCR ⁇ chain are selected for introduction into T cells.
  • Parent V ⁇ gene containing TCR ⁇ chain may be identified within the sorted cell population using V ⁇ gene specific primers for PCR.
  • V ⁇ gene specific primers for PCR One concern associated with enhancing the affinity of antigen-specific TCRs in vitro is that some modifications might increase the affinity of the receptor for MHC only, rather than peptide/MHC, thereby increasing the likelihood that the TCR will be autoreactive. Restricting the candidate TCR ⁇ chains to those containing the parent V ⁇ gene increases the likelihood of retaining the TCR CDR1 and CDR2 domains that contact the MHC, and limiting variability to CDR3.
  • viral vectors such as retroviral vectors and lentiviral vectors, are suitable for introducing the nucleic acid sequences encoding the various TCR ⁇ chains and/or the parent TCR ⁇ into T cells.
  • the viral vector further comprises a gene marker for transduction (e.g. green fluorescent protein).
  • Cells that are capable of expressing a TCR on the cell surface are used for transformation or transduction with the nucleic acid sequences encoding the various TCR ⁇ chains from the DN TCR ⁇ + thymocytes.
  • Cells that are capable of expressing a TCR on the cell surface express a CD3 molecule.
  • CD3 is a multi-protein complex of six chains that are stably associated with a TCR on the cell surface. In mammals, the complex comprises a CD3 ⁇ chain, a CD ⁇ chain, two CD3 ⁇ , and a homodimer of CD3 ⁇ chains.
  • the CD3 ⁇ , CD3 ⁇ , and CD3 ⁇ are highly related cell surface proteins of the immunoglobulin superfamily containing a single immunoglobulin domain.
  • the transmembrane regions of CD3 ⁇ , CD3 ⁇ , and CD3 ⁇ are negatively charged, which is a characteristic that allows these chains to associate with the positively charged TCR chains.
  • the cytoplasmic domains of the CD3 ⁇ , CD3 ⁇ , and CD3 ⁇ chains contain immunoreceptor tyrosine-based activation motifs (ITAMs) that allow them to associate with cytosolic protein tyrosine kinases following receptor stimulation and thereby signal to the cell interior.
  • ITAMs immunoreceptor tyrosine-based activation motifs
  • CD3 proteins are required for cell-surface expression of the TCR ( see Janeway et al., Immunobiology: The Immune System in Health and Disease, 3rd Ed., Current Biology Publications, p. 4:39, 1997 ).
  • cells that are capable of expressing a TCR on the cell surface are T cells, including primary cells or cell lines derived from human, mouse, rat, or other mammals. If obtained from a mammal, a T cell can be obtained from numerous sources, including blood, bone marrow, lymph node, thymus, or other tissues or fluids. A T cell may be enriched or purified. T cell lines are well known in the art, some of which are described in Sandberg et al., 2000, Leukemia 21:230-237 . In certain embodiments, T cells which lack endogenous expression of TCR ⁇ and ⁇ chains are used.
  • T cells may naturally lack endogenous expression of TCR ⁇ and ⁇ chains or may have been modified to block expression (e.g ., T cells from a transgenic mouse that does not express TCR ⁇ and ⁇ chains or a cell line that has been manipulated to inhibit expression of TCR ⁇ and ⁇ chains).
  • T cells from a transgenic mouse that does not express TCR ⁇ and ⁇ chains or a cell line that has been manipulated to inhibit expression of TCR ⁇ and ⁇ chains.
  • 58 ⁇ - ⁇ - cells a murine T cell line that lacks endogenous TCR ⁇ and TCR ⁇ chains, is used ( Letourneur and Malissen, 1989, Eur. J. Immunol. 19:2269-74 ).
  • H9 T cell line is used (Catalog # HTB-176, ATCC, Manassas, VA).
  • cells that capable of expressing a TCR on the cell surface are not T cells or cells of a T cell lineage, but cells that have been modified to express CD3, enabling cell surface expression of a TCR (e.g., 293 cells or 3T3 cells).
  • a TCR e.g., 293 cells or 3T3 cells.
  • MHC-peptide tetramer staining features a tetramer of MHC molecules, each comprising an identical peptide having an amino acid sequence that is cognate ( e.g ., identical or related to) at least one antigen, wherein the complex is capable of binding T cells specific for the cognate antigen.
  • MHC molecules may be tagged with a biotin molecule.
  • Biotinylated MHC/peptides are tetramerized by the addition of streptavidin, which is typically fluorescently labeled. The tetramer may be detected by flow cytometry via the fluorescent label.
  • MHC-peptide tetramer staining methods for detecting antigen specific T cells are well known in the art ( e.g., Altman et al, 1996, Science 274:94-96 ; Kalergis et al., 2000, J. Immunol. Methods 234:61-70 ; Xu and Screaton, 2002, J. Immunol. Methods 268:21-8 ; James et al., J. Vis. Exp.25:1167 ).
  • the MHC-peptide tetramer comprises MHC Class I molecules. In other embodiments, the MHC-peptide tetramer comprises MHC Class II molecules. In further embodiments, the same peptide antigen used the culture step of the disclosed method is the same as the peptide incorporated into the MHC-peptide tetramer. In other embodiments, the MHC molecule expressed by the stromal cells in the culture step of the disclosed method is the same as an MHC molecule in the MHC-peptide tetramer. MHC-peptide tetramer stained cells may be sorted by flow cytometry one or more times. A first sort may select for transduced cells expressing a detectable transduction marker (e.g., green fluorescent protein).
  • a detectable transduction marker e.g., green fluorescent protein
  • the transduction positive cells may also be sorted one or more times for cells that express the same V ⁇ chain as the parent TCR. It will be apparent to one skilled in the art that a subset of these sorts, or single or multiple cell sorts can be designed using different combinations of cell surface or transduction markers, in order to identify the desired subpopulation of cells.
  • An enhanced affinity TCR is identified by comparing the binding affinity of a candidate TCR ⁇ with the parent TCR ⁇ .
  • Antigen-specific T cells may then be cloned and sequenced using standard molecular biology techniques.
  • Candidate TCR ⁇ clones may then be used to transduce T cells comprising the parent TCR ⁇ chain and MHC-peptide tetramer staining may be used to compare staining levels with the parent TCR ⁇ , as previously described.
  • Increased staining observed with a candidate TCR ⁇ may be indicative of enhanced affinity as compared with the parent TCR ⁇ .
  • the parent TCR ⁇ was codon-optimized for increased expression in the T cell, direct comparison of tetramer staining levels with the candidate TCR ⁇ may not be possible.
  • Candidate TCR ⁇ chains may also be codon optimized for direct comparison with the parent TCR ⁇
  • a candidate TCR ⁇ has enhanced affinity compared to a parent TCR ⁇ if it has stronger binding to the peptide antigen than the parent TCR ⁇ .
  • Enhanced affinity may be indicated by a TCR with a K a (equilibrium association constant) for the target antigen higher than that of the parent TCR, a TCR with a K D (dissociation constant) for the target antigen less than that of the parent TCR, or with an off-rate (K off ) for the target antigen less than that of the wild type (or parent) TCR.
  • enhanced affinity TCRs generated by methods disclosed herein are provided.
  • An enhanced affinity TCR may be cell-bound (e.g ., expressed on the surface of a mature T cell) or in soluble form.
  • enhanced affinity TCRs may be codon optimized to enhance expression in T cells ( Scholten et al., 2006, Clin. Immunol. 119:135-145 ).
  • enhanced affinity TCRs may also be a component of a fusion protein, which may further comprise a cytotoxic component (e.g. , chemotherapeutic drugs such as vindesine, antifolates; bacterial toxins, ricin, anti-virals), which is useful for specific killing or disabling of a cancer cell or infected cell or a detectable component (e.g. , biotin, fluorescent moiety, radionuclide), which is useful for imaging cancer cells, infected cells, or tissues under autoimmune attack.
  • a cytotoxic component e.g. , chemotherapeutic drugs such as vindesine, antifolates; bacterial toxins, ricin, anti-virals
  • a detectable component e.g. , biotin, fluorescent moiety, radionuclide
  • Enhanced affinity TCRs generated by the methods of the present disclosure may be used to treat a disease (such as cancer, infectious disease, or autoimmune disease) in a subject by administering a composition comprising the enhanced affinity TCRs.
  • a disease such as cancer, infectious disease, or autoimmune disease
  • TCR gene therapy is a promising treatment for various types of cancer ( Morgan et al., 2006, Science 314:126-129 ; reviewed in Schmitt et al, 2009, Human Gene Therapy ; reviewed in June, 2007, J. Clin. Invest. 117:1466-1476 ) and infectious disease ( Kitchen et al., 2009, PLoS One 4:38208 ; Rossi et al., 2007, Nat. Biotechnol. 25:1444-54 ; Zhang et al., PLoS Pathog. 6:e1001018 ; Luo et al., 2011, J. Mol. Med.
  • Immunosuppressive gene therapy for autoimmune diseases using regulatory T cells comprising autoreactive TCRs is also an emerging treatment ( Fujio et al., 2006, J. Immunol. 177:8140-8147 ; Brusko et al., 2008, Immunol. Rev. 223:371-390 ).
  • cancers including solid tumors and leukemias are amenable to the compositions and methods disclosed herein.
  • Types of cancer that may be treated include: adenocarcinoma of the breast, prostate, and colon; all forms of bronchogenic carcinoma of the lung; myeloid; melanoma; hepatoma; neuroblastoma; papilloma; apudoma; choristoma; branchioma; malignant carcinoid syndrome; carcinoid heart disease; and carcinoma ( e.g ., Walker, basal cell, basosquamous, Brown-Pearce, ductal, Ehrlich tumor, Krebs 2, merkel cell, mucinous, non-small cell lung, oat cell, papillary, scirrhous, bronchiolar, bronchogenic, squamous cell, and transitional cell).
  • carcinoma e.g ., Walker, basal cell, basosquamous, Brown-Pearce, ductal, Ehrlich
  • cancers include: histiocytic disorders; leukemia; histiocytosis malignant; Hodgkin's disease; immunoproliferative small; non-Hodgkin's lymphoma; plasmacytoma; reticuloendotheliosis; melanoma; chondroblastoma; chondroma; chondrosarcoma; fibroma; fibrosarcoma; giant cell tumors; histiocytoma; lipoma; liposarcoma; mesothelioma; myxoma; myxosarcoma; osteoma; osteosarcoma; chordoma; craniopharyngioma; dysgerminoma; hamartoma; mesenchymoma; mesonephroma; myosarcoma; ameloblastoma; cementoma; odontoma; teratoma;
  • cancers are also contemplated as amenable to treatment: adenoma; cholangioma; cholesteatoma; cyclindroma; cystadenocarcinoma; cystadenoma; granulosa cell tumor; gynandroblastoma; hepatoma; hidradenoma; islet cell tumor; Leydig cell tumor; papilloma; sertoli cell tumor; theca cell tumor; leimyoma; leiomyosarcoma; myoblastoma; myomma; myosarcoma; rhabdomyoma; rhabdomyosarcoma; ependymoma; ganglioneuroma; glioma; medulloblastoma; meningioma; neurilemmoma; neuroblastoma; neuroepithelioma; neurofibroma; neuroma; paraganglioma;
  • the types of cancers that may be treated also include: angiokeratoma; angiolymphoid hyperplasia with eosinophilia; angioma sclerosing; angiomatosis; glomangioma; hemangioendothelioma; hemangioma; hemangiopericytoma; hemangiosarcoma; lymphangioma; lymphangiomyoma; lymphangiosarcoma; pinealoma; carcinosarcoma; chondrosarcoma; cystosarcoma phyllodes; fibrosarcoma; hemangiosarcoma; leiomyosarcoma; leukosarcoma; liposarcoma; lymphangiosarcoma; myosarcoma; myxosarcoma; ovarian carcinoma; rhabdomyosarcoma; sarcoma; neoplasms; nerofibromatosis
  • Additional B cell cancers include small lymphocytic lymphoma, B-cell prolymphocytic leukemia, lymphoplasmacytic lymphoma, splenic marginal zone lymphoma, plasma cell myeloma, solitary plasmacytoma of bone, extraosseous plasmacytoma, extra-nodal marginal zone B-cell lymphoma of mucosa-associated (MALT) lymphoid tissue, nodal marginal zone B-cell lymphoma, follicular lymphoma, mantle cell lymphoma, diffuse large B-cell lymphoma, mediastinal (thymic) large B-cell lymphoma, intravascular large B-cell lymphoma, primary effusion lymphoma, Burkitt's lymphoma/leukemia, B-cell proliferations of uncertain malignant potential, lymphomatoid granulomatosis, and post-transplant lymphoproliferative disorder.
  • MALT mucosa-associated lymphoid tissue
  • Infectious viruses include eukaryotic viruses (e.g ., adenovirus, bunyavirus, herpesvirus, papovavirus, paramyxovirus, picornavirus, rhabdovirus (e.g ., Rabies), orthomyxovirus (e.g ., influenza), poxvirus ( e.g ., Vaccinia), reovirus, retroviruses, lentiviruses ( e.g. , HIV), flaviviruses ( e.g ., HCV) and the like).
  • eukaryotic viruses e.g ., adenovirus, bunyavirus, herpesvirus, papovavirus, paramyxovirus, picornavirus, rhabdovirus ( e.g ., Rabies), orthomyxovirus ( e.g ., influenza), poxvirus ( e.g ., Vaccinia), reovirus, retroviruses, lentiviruses (
  • Treatment refers to medical management of a disease, disorder, or condition of a subject (i.e., individual who may be a human or non-human mammal (e.g., primate, mouse, rat)).
  • a subject i.e., individual who may be a human or non-human mammal (e.g., primate, mouse, rat)).
  • an appropriate dose and treatment regimen provide the herein described enhanced affinity TCRs, and optionally, an adjuvant, in an amount sufficient to provide therapeutic or prophylactic benefit.
  • Therapeutic and prophylactic benefits include improved clinical outcome; lessening or alleviation of symptoms associated with the disease; decreased occurrence of symptoms; improved quality of life; longer disease-free status; diminishment of extent of disease, stabilization of disease state; delay of disease progression; remission; survival; or prolonging survival.
  • compositions including the enhanced affinity receptors may be administered in a manner appropriate to the disease or condition to be treated (or prevented) as determined by persons skilled in the medical art.
  • An appropriate dose, suitable duration, and frequency of administration of the compositions will be determined by such factors as the condition of the patient, size, type and severity of the disease, particular form of the active ingredient, and the method of administration.
  • enhanced affinity TCRs of the instant disclosure may be used in diagnostic methods or imaging methods, including these methods used in relation to the indications or conditions identified herein.
  • TCR transgenic thymocytes efficiently differentiate into a " ⁇ like" CD4 - CD8 - CD24 - TCR ⁇ + lineage when exposed to their cognate antigen in OP9-DL1 cultures.
  • progenitor thymocytes expressing only the TCR ⁇ chain from a T cell clone specific for the tumor antigen WT1 can also differentiate into this mature TCR ⁇ + lineage in OP9-DL1 culture.
  • a library of TCR ⁇ chains was generated from a population of DN TCR ⁇ + cells sorted from these cultures, and screened for WT1 MHC tetramer reactivity when paired with the antigen-specific TCR ⁇ chain. Using this approach, several TCR ⁇ chains were identified that can pair with an antigen-specific TCR ⁇ chain to generate TCRs with up to 10-fold higher affinity for WT1 peptide as compared to the original TCR.
  • Example 1 Engagement of peptide agonist during differentiation on OP9-DL1 cells can drive differentiation of mature TCR ⁇ + DN cells from T cell progenitors purified from TCR transgenic mice.
  • TCR ⁇ - CD4 - CD8 - CD117 + CD44 + DN1 and DN2 progenitor thymocytes were sorted from transgenic OT-1 mice (express TCR specific for ovalbumin peptide sequence SIINFEKL (SEQ ID NO:1) presented on MHC Class I H-2K b ; Stock #003831, Jackson Laboratory, ME; see also Hogquist et al., 1994, Cell 76:17-27 ) and cultured with OP9-DL1 cells ( Schmitt et al., 2002, Immunity 17:749-756 ; U.S.
  • Patent No. 7,575,925 transduced to express the mouse MHC Class I molecule H-2K b , either in the absence of peptide, or with increasing concentrations of ovalbumin-specific peptide (SEQ ID NO:1) for 20 days and analyzed at various time points by flow cytometry.
  • double positive (DP) T cells could be detected by day 16, and constituted a major fraction of the culture by day 20 ( Fig. 1A ).
  • the development or survival of DP T cells was diminished by even very low concentrations of peptide (0.0001 ⁇ M), and DP were completely absent from cultures containing 0.01 ⁇ M or more of peptide ( Fig. 1A ), demonstrating that DP cells are negatively selected by strong agonist signaling in OP9-DL1 cultures.
  • TCR ⁇ + DN cells In order to determine whether increasingly strong agonist signals drive the development of TCR ⁇ + DN cells, the DN population was analyzed for expression of CD24, a maturation marker that is expressed at high levels on all immature progenitor T cell populations, and TCR ⁇ . The majority of cells were found to express high levels of CD24 and to lack TCR ⁇ expression at day 5 ( Fig.
  • ⁇ 60% of all DN cells were TCR ⁇ + CD24 - from cultures containing 0.01 ⁇ M or 1.0 ⁇ M peptide, while in cultures that received no peptide or a low concentration (0.0001 ⁇ M) of peptide, only ⁇ 20% of DNs were TCR ⁇ + CD24 - , and close to 50% were TCR ⁇ - ( Fig. 1B , 1C ). Furthermore, when the level of TCR surface expression is compared between the different culture conditions, the TCR ⁇ + cells that developed in response to high levels of peptide expressed higher levels of TCR ⁇ on the cell surface ( Fig. 1C ).
  • TCR ⁇ + DN cells in cultures without added peptide is due to cross-reactivity with other peptide-MHC ligands in the OP9-DL1 culture system.
  • CD69 - DP cells that have not yet been positively selected were sorted from B6 or OT-1 thymus and cultured in the presence or absence of ovalbumin SIINFEKL peptide (SEQ ID NO:1).
  • B6 DP cells were unaffected by the presence of SIINFEKL peptide (SEQ ID NO:1), but when OT-1 DP thymocytes were cultured on OP9-DL1 cells in the presence SIINFEKL (SEQ ID NO:1), all the hallmarks of negative selection were observed, including a massive loss of cellularity and co-receptor down-modulation ( Fig. 2 ). Importantly, the DN cells observed in these cultures were uniformly TCR negative ( Fig. 2 ).
  • Example 2 A transgenic TCR ⁇ chain pairs with endogenous TCR ⁇ chains to drive the development of DN CD24 - TCR ⁇ + " ⁇ warmtha-be" cells in the OP9-DL1 culture system
  • CD4 - CD8 - CD117 + CD44 + DN1 and DN2 progenitor thymocytes were sorted from B6 mice and transduced with a TCR ⁇ chain from the Wilm's tumor antigen (WT1) specific T cell clone 3D that had previously been identified as an affinity enhanced variant isolated from a saturation mutagenesis library of the CDR3 region of the 3D ⁇ .
  • WT1 Wilm's tumor antigen
  • DN cells within the hCD2 negative fraction contained few TCR ⁇ + cells, regardless of the presence of peptide in the culture conditions.
  • the hCD2 positive fraction (which expressed the 3D ⁇ gene) from cultures that did not receive peptide contained 6.8% TCR ⁇ + cells, and the number of TCR ⁇ + cells increased to 16.6% when 1.0 ⁇ M WT1 peptide was added ( Fig. 3A ).
  • 3D ⁇ -transduced CD4 - CD8 - CD117 + CD44 + DN1 and DN2 progenitor thymocytes were differentiated on OP9-DL1 cells expressing mouse MHC Class 1 H-2D b and also transduced to express WT1.
  • Non-adherent cells were collected at for several days up to day 21 and sorted for hCD2 + CD4 - CD8 - TCR ⁇ + cells into TRIzol reagent (Invitrogen) ( Fig. 3B ). Cell sorts from individual days were pooled; RNA was purified, and cDNA was generated.
  • the parent 3D TCR uses the Vb10 variable region.
  • All four candidate clones bound MHC-WT1 peptide tetramer when transduced into 3D ⁇ + 58 -/- cells, although clone#4 bound MHC-WT1 peptide tetramer at significantly lower levels than the others and was not analyzed further.
  • the parent 3D ⁇ chain had previously been codon-optimized, and therefore expressed higher levels of TCR at the cell surface, precluding direct comparison of tetramer staining levels between 3D ⁇ and the isolated clones.
  • TCR ⁇ library TCR ⁇ chains that share the same variable domain (Vb10) in order to restrict variablility to CDR3.
  • Vb10 variable domain
  • transduced 58 -/- cells were stained with a panel of MHC H-2D b tetramers (peptides: WT1, GP33, E4, MESN, SQV).
  • Human hematopoietic progenitor cells readily proliferate and differentiate in OP9-DL1 culture to a stage of human T cell development characterized by the phenotype CD34 + CD1a + CD4 + ( La Motte-Mohs et al., 2005, Blood 105:1431-1439 ), at which point they are undergoing TCR gene rearrangements at the ⁇ , ⁇ , and ⁇ loci ( Spits, 2002, Nat. Rev. Immunol. 2:760-772 ).
  • the endogenous TCR ⁇ chains are cloned by purifying total RNA, performing full-length RACE RT-PCR with C- ⁇ 1 or C- ⁇ 2 primers, and cloning the PCR products into the pENTRTM/D-TOPO® vector (Invitrogen), which allows directional TOPO-cloning and incorporates attL sites that allow rapid and efficient transfer to the retroviral vector Mig-attR (a variant of MigR1 ( Pear et al.,1998, Blood 92:3780-3792 ) that contains attR sites for insertion of gene of interest) using Invitrogen's Gateway® technology recombination system.
  • the products of the recombination reaction are electroporated into high efficiency bacteria, and colonies are scraped together and maxiprepped to generate a retroviral library of potentially WT1-reactive TCR ⁇ chains.
  • TCR ⁇ chains and the parental C4 ⁇ are transduced into H9-C4 ⁇ cells and the relative affinities for the MHC-WT1 peptide tetramer will be calculated by staining transduced cells with serial 2-fold dilutions of PE-conjugated tetramers (as described in Example 2). Affinity values are determined by fitting the MFI for each dilution to a binding curve by non-linear regression and KD defined as tetramer concentration yielding half-maximal binding. TCR ⁇ chains that can pair with C4 TCR ⁇ to generate a TCR with higher affinity by MHC-peptide tetramer staining than the wildtype C4 receptor are further characterized for safety and efficacy.
  • hematopoietic progenitor/stem cells were purified from the bone marrow of B6 mice and transduced to express the TCR ⁇ chain from either the high affinity WT1 specific 3D-PYY TCR or the low affinity mesothelin specific TCR 7431.
  • the 3D-PYY TCR is a higher affinity TCR engineered from the 3D TCR, identified using a T cell display system and selection with WT1/D b Ig DimerX (BD Biosciences) ( Stone et al., 2011, J. Immunol. 186:5193-5200 ; Chervin et al., 2008, J. Immunol. Methods 339:175-184 ).
  • Splenocytes from 3D-PYY ⁇ and 7431 ⁇ retrogenic mice were stimulated with WT1 peptide and Mesothelin peptide, repectively, and cultured in vitro in the presence of IL-2 for 6 days.
  • IL-2 was added to the culture in order to potentially expand antigen specific cells so they could be detected by tetramer staining.
  • Cultures were analyzed for CD4 and CD8 expression by flow cytometry within the TCR ⁇ + gate, as well as for expression of the parental TCR V ⁇ gene ( Figure 7 ). Again, enrichment for the parental V ⁇ gene family is observed, especially for the high affinity 3D-PYY.

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